Advice with an Unannotated gene

Question

[jafisep314]

Hi all, I am currently trying to characterize variants (from WGS) in a gene that is not annotated by Variant Effect Predictor (VEP). I am quite new to bioinformatics, would y'all have any advice on how to start?

[manaswwm]

If you are talking about annotating variants within a genome that already has an annotation file (GTF/GFF) but there is no variant annotation available then you could try using SnpEff (http://pcingola.github.io/SnpEff/se_buildingdb/). I am not aware how this is possible for single gene, except if you are talking exclusively about SNPs, in which case I imagine an easier trick would be to start from the ORF and try to write a code which looks at the effect of variants on codon-by-codon basis